panModule: detecting conserved modules in the variable regions of a pangenome graph

The recent years have seen the rise of pangenomes as comparative genomic tools to better understand the evolution of gene content among microbial genomes in close phylogenetic groups such as species. While the core or persistent genome is often well-known as it includes essential or ubiquitous genes, the variable genome is usually less characterized and includes many genes with unknown functions even among the most studied organisms. It gathers important genes for strain adaptation that are acquired by horizontal gene transfer. Here, we introduce panModule, an original method to identify conserved modules in pangenome graphs built from thousands of microbial genomes. These modules correspond to synteny blocks composed of consecutive genes that are conserved in a subset of the compared strains. Identifying conserved modules can provide insights on genes involved in the same functional processes, and as such is a very helpful tool to facilitate the understanding of genomic regions with complex evolutionary histories. The panModule method was benchmarked on a curated dataset of conserved modules in Escherichia coli genomes. Its use was illustrated through a study of a high pathogenicity island in Klebsiella pneumoniae that allowed a better understanding of this region. panModule is freely available and accessible through the PPanGGOLiN software suite (https://github.com/labgem/PPanGGOLiN).

Nuclear Dynamics and Chromatin Structure: Implications for Pancreatic Cancer

Changes in nuclear shape have been extensively associated with the dynamics and functionality of cancer cells. In most normal cells, nuclei have a regular ellipsoid shape and minimal variation in nuclear size; however, an irregular nuclear contour and abnormal nuclear size is often observed in cancer, including pancreatic cancer. Furthermore, alterations in nuclear morphology have become the ‘gold standard’ for tumor staging and grading. Beyond the utility of altered nuclear morphology as a diagnostic tool in cancer, the implications of altered nuclear structure for the biology and behavior of cancer cells are profound as changes in nuclear morphology could impact cellular responses to physical strain, adaptation during migration, chromatin organization, and gene expression. Here, we aim to highlight and discuss the factors that regulate nuclear dynamics and their implications for pancreatic cancer biology.

PSYCHOPHYSIOLOGICAL RESEARCH METHODS EFFECTIVENESS OF ELECTRIC TRAIN DRIVERS PROFESSIONAL PERFORMANCE ASSESSMENT

Electric train driver work requires visual, auditory, tactile systems functioning high level, as well as mentality. These requirements caused the study directed to analyze the professional performance effectiveness these indicators, psychophysiological parameters including, for training and retraining in train driver (assistant train driver) profession. The research was carried out in the base of the training centers of professional qualifications of JSC «Russian Railways», 106 people were examined (age 27.2± 5.4 years) who were trained to perform all operations under work as train driver: first theoretically, then practically by special simulators use. There were evaluated: cardiovascular system state, complex visual-motor reaction time, «Landolt Ring» correction test as well as psychological methods of personal properties testing: reflection, self-regulation of behavior; the method of differentiated assessment of working capacity reduced. The dependence of working capacity of factor’s complex are determined. There are: organism’s functional state, psycho-emotional strain, adaptation mechanisms, motivational involvement, and target aspiration. Based on obtained data a set of promising methods has been determined to identify the possibility of reliable of driver operation and adjustment of his activities aimed at improving self-regulation skills as one of the main criteria for reliability of work.

Development of lactic acid fermented, probiotic sour cherry juice

Nowadays, demand for products which beyond the overall nutritional value have a feature that protects the consumer health, have increased. Several studies have proved that fruit juices can become a suitable carrier or medium for probiotic organisms. Therefore, the aim of our study was to investigate the possibility of the probiotication of sour cherry juice (SCJ) by fermentation with probiotic starter culture. During the fermentation 9 Lactobacillus strains were used and Újfehértói fürtös sour cherry species as raw material. To reach the recommended probiotic cell count we investigated the pH adjustment, supplementation of nutrients, the effect of dilution, and strain adaptation to SCJ. In our study the properties of the strains – such as reproduction and metabolism – and its effect on the raw material were investigated. A significant difference was observed between the number of viable cells of certain Lactobacillus strains, that is important in point of view of the development of probiotic-containing products. Furthermore, the lactic acid fermented SCJ can enhance the polyphenol content and antioxidant activity to promote the health of consumers.

Short-Term Bone Formation is Greatest Within High Strain Regions of the Human Distal Radius: A Prospective Pilot Study

Bone adaptation is understood to be driven by mechanical strains acting on the bone as a result of some mechanical stimuli. Although the strain/adaptation relation has been extensively researched using in vivo animal loading models, it has not been studied in humans, likely due to difficulties in quantifying bone strains and adaptation in living humans. Our purpose was to examine the relationship between bone strain and changes in bone mineral parameters at the local level. Serial computed tomography (CT) scans were used to calculate 14 week changes in bone mineral parameters at the distal radius for 23 women participating in a cyclic in vivo loading protocol (leaning onto the palm of the hand), and 12 women acting as controls. Strains were calculated at the distal radius during the task using validated finite element (FE) modeling techniques. Twelve subregions of interest were selected and analyzed to test the strain/adaptation relation at the local level. A positive relationship between mean energy equivalent strain and percent change in bone mineral density (BMD) (slope = 0.96%/1000 με, p < 0.05) was observed within experimental, but not control subjects. When subregion strains were grouped by quartile, significant slopes for quartile versus bone mineral content (BMC) (0.24%/quartile) and BMD (0.28%/quartile) were observed. Increases in BMC and BMD were greatest in the highest-strain quartile (energy equivalent strain > 539 με). The data demonstrate preliminary prospective evidence of a local strain/adaptation relationship within human bone. These methods are a first step toward facilitating the development of personalized exercise prescriptions for maintaining and improving bone health.